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[173871_at] spectrin alpha chain

Description CEK033F4R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=K10B3.10 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D33616 /WB_GENE_ID=K10B3.10 /WP=CE07373 /CHR=X /FEA=Genomic Cluster /GEN=spc-1 /DEF=spectrin alpha chain; C.elegans cDNA clone yk33f4 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 51      6grp_high1_10_10 > 16      4grp_highest_8_8 > 48      4grp_high_8_8 > 42      6grp_highest_nonorm > 03      6grp_total > 16      4grp_total > 53      6grp_highest_sub > De      6grp_cgc > 13      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3076
1 2 3 4 range
A 4274.1
(3)
P 		3118.8
(0.7)
P 		2643.8
(-0.2)
P 		1245.8
(-3)
P 		3028
B 3525
(3)
P 		3239.3
(2.2)
P 		1910.4
(-1.8)
P 		1507
(-3)
P 		2018
C 3989.3
(3)
P 		3062.2
(1)
P 		2691
(0.2)
P 		1198.5
(-3)
P 		2791
avr 3929.5
(3) 		3140.1
(1.2) 		2415.1
(-0.5) 		1317.1
(-3) 		2612

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3386
1 2 3 4 5 6 range
A 4764.2
(3)
P 		3497.2
(0.4)
P 		1952.7
(-2.9)
P 		1889.6
(-3)
P 		2349.9
(-2)
P 		2258.3
(-2.2)
P 		2875
B 4300.1
(3)
P 		3690.6
(1.6)
P 		2010.1
(-2.2)
P 		2469.5
(-1.1)
P 		1636.4
(-3)
P 		1840.6
(-2.5)
P 		2664
C 3829.8
(3)
P 		3310.9
(1.7)
P 		2567.1
(-0.1)
P 		1715.5
(-2.2)
P 		1962.1
(-1.6)
P 		1378.5
(-3)
P 		2451
avr 4298
(3) 		3499.6
(1.1) 		2176.6
(-2.1) 		2024.9
(-2.5) 		1982.8
(-2.6) 		1825.8
(-3) 		2472
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1374
1 2 3 4 range
A 1556.2
(3)
P 		677
(-0.8)
P 		691.2
(-0.8)
P 		182.4
(-3)
P 		1374
B 1124.1
(3)
P 		800
(0.6)
P 		442.7
(-2.1)
P 		321.1
(-3)
P 		803
C 1320.6
(3)
P 		880.4
(0.6)
P 		937.9
(0.9)
P 		202.1
(-3)
P 		1119
avr 1333.6
(3) 		785.8
(0) 		690.6
(-0.5) 		235.2
(-3) 		1098

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1151
1 2 3 4 5 6 range
A 878.2
(0.3)
P 		1243.8
(3)
P 		425.3
(-3)
P 		479.2
(-2.6)
P 		709.1
(-0.9)
P 		549.8
(-2.1)
P 		819
B 1496.2
(3)
P 		1228.4
(1.4)
P 		488.1
(-3)
P 		654.1
(-2)
P 		664.8
(-1.9)
P 		686.4
(-1.8)
P 		1008
C 1419.6
(3)
P 		1010.2
(0.7)
P 		653.4
(-1.3)
P 		345
(-3)
P 		634.9
(-1.4)
P 		461.4
(-2.4)
P 		1075
avr 1264.7
(3) 		1160.8
(2.2) 		522.3
(-2.8) 		492.8
(-3) 		669.6
(-1.6) 		565.9
(-2.4) 		772
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173871_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26201
Sequence Type Exemplar sequence
Representative Public ID CEK033F4R NCBI
Target Description CEK033F4R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=K10B3.10 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D33616 /WB_GENE_ID=K10B3.10 /WP=CE07373 /CHR=X /FEA=Genomic Cluster /GEN=spc-1 /DEF=spectrin alpha chain; C.elegans cDNA clone yk33f4 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
Annotation Method Description
Annotation Description This probe set was annotated using the Matching Probes based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_076136(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076136 NCBI Caenorhabditis elegans SPeCtrin family member (spc-1) (spc-1) mRNA, complete cds. 11/11 None
K10B3.10 ENSEMBL cdna:known chromosome:CEL140:X:3117430:3127061:-1 gene:K10B3.10 11/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:3117448-3127053(-) 100.0 100.0
Public Domain and Genome References
Gene Title spectrin alpha chain
Gene Symbol spc-1
Ensembl K10B3.10
Entrez Gene 180603 Entrez gene
SwissProt Q21408 EMBL-EBI
WormBase CE07373 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1606042_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) cfa
CANINE:1583448_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) cfa
CANINE:1582820_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) cfa
CANINE_2:CFA.11603.1.A1_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) cfa
CANINE_2:CFA.18239.1.S1_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) cfa
CANINE_2:CFA.196.1.S1_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) cfa
CANINE_2:CFAAFFX.30684.1.S1_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) cfa
CANINE_2:CFAAFFX.30684.1.S1_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) cfa
DROSOPHILA_2:1626349_AT Spectrin dm
CHICKEN:GGA.11413.1.S1_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) gga
CHICKEN:GGA.4441.1.S1_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) gga
CHICKEN:GGAAFFX.21304.1.S1_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) gga
HG-U133_PLUS_2:208611_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133A:208611_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-FOCUS:208611_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133A_2:208611_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HUGENEFL:J05243_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133_PLUS_2:214925_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133A_2:214925_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133A:214925_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
U133_X3P:HS.77196.2.A1_3P_A_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
U133_X3P:HS.321666.0.S1_3P_S_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U95AV2:33833_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U95D:89935_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133_PLUS_2:214926_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133A_2:214926_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133A:214926_AT spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133_PLUS_2:215235_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133A_2:215235_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133A:215235_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HU35KSUBB:RC_H15913_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
U133_X3P:HS.31396.0.A1_3P_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133_PLUS_2:241150_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U133B:241150_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U95C:64221_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
HG-U95E:90760_AT Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) hs
RG-U34A:AF084186_S_AT hypothetical gene supported by NM_171983 rn
RG-U34B:RC_AA849856_AT hypothetical gene supported by NM_171983 rn
RAE230A:1370838_S_AT hypothetical gene supported by NM_171983 rn
RAT230_2:1370838_S_AT hypothetical gene supported by NM_171983 rn
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
5509 calcium ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB53876 Spectrin protein 1 [Caenorhabditis elegans] ref|NP_508537.1| SPeCtrin family member (spc-1) [Caenorhabditis elegans] 0.0
blast CAE68383 Hypothetical protein CBG14139 [Caenorhabditis briggsae] 0.0
blast XP_623691 PREDICTED: similar to GA15168-PA [Apis mellifera] 0.0
Protein Domains
Database ID Description E-Value
scop a.2.7.Seryl-tRNA synthetase (SerRS) All alpha proteins; Long alpha-hairpin; tRNA-binding arm; Seryl-tRNA synthetase (SerRS) 5.80000019073486
Pfam IPR002048 EMBL-EBI Calcium-binding EF-hand 1.3E-5
Pfam IPR002048 EMBL-EBI Calcium-binding EF-hand 4.7E-6
Pfam IPR001452 EMBL-EBI SH3 4.1E-20
Pfam IPR002017 EMBL-EBI Spectrin repeat 0.43
Pfam IPR002017 EMBL-EBI Spectrin repeat 9.0E-30
Pfam IPR002017 EMBL-EBI Spectrin repeat 3.0E-27
Pfam IPR002017 EMBL-EBI Spectrin repeat 4.2E-30
Pfam IPR002017 EMBL-EBI Spectrin repeat 2.5E-24
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.3E-33
Pfam IPR002017 EMBL-EBI Spectrin repeat 9.3E-31
Pfam IPR002017 EMBL-EBI Spectrin repeat 3.7E-31
Pfam IPR002017 EMBL-EBI Spectrin repeat 4.8E-28
Pfam IPR002017 EMBL-EBI Spectrin repeat 6.5E-21
Pfam IPR002017 EMBL-EBI Spectrin repeat 0.11
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.0E-24
Pfam IPR002017 EMBL-EBI Spectrin repeat 3.1E-32
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.3E-30
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.3E-29
Pfam IPR002017 EMBL-EBI Spectrin repeat 3.9E-28
Pfam IPR002017 EMBL-EBI Spectrin repeat 5.2E-29
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.1E-32
Pfam IPR002017 EMBL-EBI Spectrin repeat 4.3E-28
Pfam IPR002017 EMBL-EBI Spectrin repeat 1.6E-30
Pfam IPR002017 EMBL-EBI Spectrin repeat 7.3E-20
Pfam IPR002017 EMBL-EBI Spectrin repeat 8.7E-11
Sequence
Target Sequence 
>C. ELEGANS:173871_AT
agagctaatctcgccaattgtcatatgattttaaatttctcgtttcttcctaccactggt
cacttgttcctccatccaacagtttattaatactcccagataacgttttaaatgcaaaag
gaaaagtataatttgtacgcttatttgccctccccgctttttctttgaatattttatttt
tactttgtcactgtctttttataatcccatctttcacaaaagcaaaacacaatagcatta
tattaatagttttatgcaacaaactattcattattttatgaatggatttctcttcctttc
cgaataaagtcctgccatttcatgtaatgtccctaaacaaaaacactgatttctttattc
cattccagtcagaaaatcggtcatgttttgttttgatgtgcttttcattttgtactccac
ccaaaatcattgctga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGAGCTAATCTCGCCAATTGTCATA 626 69 7290 Antisense
GTTCCTCCATCCAACAGTTTATTAA 550 441 7355 Antisense
ATAATTTGTACGCTTATTTGCCCTC 170 25 7417 Antisense
TTTTACTTTGTCACTGTCTTTTTAT 387 675 7467 Antisense
GTCTTTTTATAATCCCATCTTTCAC 454 469 7482 Antisense
TGAATGGATTTCTCTTCCTTTCCGA 126 565 7568 Antisense
TCCTTTCCGAATAAAGTCCTGCCAT 641 591 7583 Antisense
GTCCTGCCATTTCATGTAATGTCCC 280 477 7598 Antisense
GATTTCTTTATTCCATTCCAGTCAG 56 429 7637 Antisense
GTGCTTTTCATTTTGTACTCCACCC 577 479 7687 Antisense
GTACTCCACCCAAAATCATTGCTGA 304 459 7701 Antisense
Sequence Source Affymetrix Proprietary Database